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Distinct Modes of Mediator-Dependent Transcription at Heat Shock Protein Genes and Nuclear Stress Bodies

ABSTRACT: Cells adapt to environmental stress by reprogramming gene expression. During heat stress, the transcription factor HSF1 translocates into the nucleus and activates heat shockâ€“responsive genes, including the lncRNA HSATIII, thereby promoting formation of nuclear stress bodies (nSBs). We show that the Mediator subunit MED26 enhances HSATIII transcription and nSB formation through a mechanism distinct from its role at canonical heat shock protein (HSP) genes. Upon heat stress, MED26-containing Mediator is recruited to both HSP loci and nSBs through interactions with HSF1 and MED15. Notably, phosphorylation of the intrinsically disordered region (IDR) of HSF1 is particularly important for Mediator recruitment to nSBs. Acute loss of MED26 leads to dissociation of both Mediator and Pol II from HSP promoters, whereas at HSATIII loci Mediator is retained despite Pol II dissociation. These results indicate that MED26 acts as molecular switch that facilitates Mediator-Pol II holo-complex assembly at nSBs and promotes nSB formation during heat stress.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Hidehisa Takahashi

PROVIDER: PXD073817 | JPOST Repository | Fri Jul 17 00:00:00 BST 2026

REPOSITORIES: jPOST

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			Action	DRS
	Li_SILAC1_N1.raw	Raw
	Li_SILAC1_N2.raw	Raw
	Li_SILAC1_N3.raw	Raw
	proteinGroups.txt	Txt

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Similar Datasets

Distinct Modes of Mediator-Dependent Transcription at Heat Shock Protein Genes and Nuclear Stress Bodies

Project description:Cells adapt to environmental stress by reprogramming gene expression. During heat stress, the transcription factor HSF1 translocates into the nucleus and activates heat shockâ€“responsive genes, including the lncRNA HSATIII, thereby promoting formation of nuclear stress bodies (nSBs). We show that the Mediator subunit MED26 enhances HSATIII transcription and nSB formation through a mechanism distinct from its role at canonical heat shock protein (HSP) genes. Upon heat stress, MED26-containing Mediator is recruited to both HSP loci and nSBs through interactions with HSF1 and MED15. Notably, phosphorylation of the intrinsically disordered region (IDR) of HSF1 is particularly important for Mediator recruitment to nSBs. Acute loss of MED26 leads to dissociation of both Mediator and Pol II from HSP promoters, whereas at HSATIII loci Mediator is retained despite Pol II dissociation. These results indicate that MED26 acts as molecular switch that facilitates Mediator-Pol II holo-complex assembly at nSBs and promotes nSB formation during heat stress.

2026-07-17 | PXD073807 | JPOST Repository

CPSF73 activation and 3’ Pol II pausing are lost during read-through transcription after heat shock [ChIP-seq]

Project description:Multiple types of cellular stress induce RNA polymerase II (Pol II) to read through normal termination sites at mRNA genes, causing long downstream regions to be transcribed. We observed strong read-through transcription downstream of thousands of genes after heat shock. Additionally, the 3’ Pol II pause that normally occurs during termination was globally lost. Heat shock also increased phosphorylation of Tyr1 and Ser2 residues in the Pol II C-terminal domain (CTD) at the 3’ ends of genes, with smaller increases observed at genes with read-through transcription. We found that 3’ RNA cleavage, a key step of transcription termination, was defective at read-through genes after heat shock; however, the CPSF73 endonuclease responsible for cleavage remained at the 3’ ends of genes. Over-expressing an activator of CPSF73 activity, RBBP6, during heat shock rescued the loss of cleavage and attenuated read-through transcription. Our data suggest that heat shock alters Pol II speed, CTD phosphorylation, and CPSF73 activity via RBBP6, contributing to a multifaceted mechanism that enables transcription to continue far downstream of normal termination sites during cellular stress.

2026-02-04 | GSE303857 | GEO

CPSF73 activation and 3’ Pol II pausing are lost during read-through transcription after heat shock [RNA-seq]

2026-02-04 | GSE303856 | GEO

The Mediator kinase module regulates transcriptional memory after heat stress by resolving blocked RNA polymerase complexes

Project description:In nature, plants are often exposed to recurring adverse environmental conditions. Acclimation to high temperature stress entails transcriptional responses that are mediated by heat-shock transcription factors (HSFs), and they are primed to better withstand subsequent stress events. This heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurring HS. However, the mechanisms by which HSFs recruit and enact the transcriptional machinery remain unclear. Here, we identified two subunits of the kinase module of the Mediator transcriptional co-regulator complex, CDK8 and MED12, as regulators of HS memory in Arabidopsis thaliana. Enhanced re-induction of gene expression after recurrent HS and physiological HS memory, as well as H3K4 methylation are compromised in cdk8 and med12 mutants. HSFA2 interacts with CDK8 during and after HS and recruits it to memory gene loci, where CDK8 binds in the promoter but also the gene body, together with core Mediator and RNA polymerase II (Pol II). Our data suggest that CDK8 resolves stalled Pol II complexes or promotes efficient recycling for subsequent cycles of transcription. As HSFA2, CDK8 is largely dispensable for the initial induction of gene expression after HS and thus promotes transcriptional memory independently of HS-dependent primary gene induction. Our findings provide a model for the complex role of the Mediator kinase module during transcriptional memory in multicellular eukaryotes through interaction with transcription factors, chromatin modifications and promotion of Pol II productivity.

2023-12-12 | GSE232094 | GEO

Mediator promotes CENP-A incorporation at fission yeast centromeres [ChIP-seq]

Project description:At Schizosaccharomyces pombe centromeres, heterochromatin formation is required for de novo incorporation of the histone H3 variant CENP-A/Cnp1, which in turn directs kinetochore assembly and ultimately chromosome segregation during mitosis. Noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (Pol II) directs heterochromatin formation via the RNAi machinery, but also through RNAiindependent RNA processing factors. Control of centromeric ncRNA transcription is therefore a key factor for proper centromere function. We here use transcriptional profiling, gene inactivation experiments, and chromatin immunoprecipitation analyses to demonstrate that the Mediator complex directs ncRNA transcription and regulates centromeric heterochromatin formation in fission yeast. Mediator co-localizes with Pol II at centromeres and loss of the Mediator subunit Med20 causes a dramatic increase in pericentromeric transcription and desilencing of the core centromere. As a consequence, heterochromatin formation is impaired both via the RNAi dependent and independent pathways, resulting in loss of CENP-A/Cnp1 from the core centromere, defect kinetochore function, and a severe chromosome segregation defect. Interestingly, the increased centromeric transcription observed in med20Δ appears to directly block CENP-A/Cnp1 incorporation and inhibition of Pol II transcription can suppress the observed phenotypes. Our data thus identify Mediator as a crucial regulator of ncRNA transcription at fission yeast centromeres and add another crucial layer of regulation to centromere function. 3 samples examined: wild type chromatin incubated with beads as the non antibody control, wild type chromatin incubated with RNA Polymerase II CTD domain antibody and Protein G beads, and TAP-Med7 cells chromatin incubated with IgG beads.

2012-11-06 | E-GEOD-35524 | biostudies-arrayexpress

The Rpd3L HDAC complex is essential for the heat stress response in yeast

Project description:To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. Global gene expression analysis showed that Rpd3 partially regulated gene expression upon heat shock. The Hsf1 and Msn2/4 transcription factors are the main regulators of gene activation in response to heat stress. RPD3-deficient cells had impaired activation of Msn2/4-dependent genes, while activation of genes controlled by Hsf1 was deacetylase independent. Rpd3 bound to heat stress-dependent promoters through the Msn2/4 transcription factors, allowing entry of RNA Pol II and activation of transcription upon stress. Finally, we found that the large, but not the small Rpd3 complex regulated cell adaptation in response to heat stress.

2010-04-23 | GSE17514 | GEO

Systematic investigation on the effect of O-GlcNAcylation on condensate formation under heat stress and recovery

Project description:O-GlcNAc is known to regulate the aggregation and condensate formation of several proteins, but how O-GlcNAc regulates protein solubilities globally has yet to be systematically investigated. Here, we employed a chemoproteomic workflow integrating selective enrichment and multiplex proteomics to quantify the solubilities of O-GlcNAcylated and non-modified proteins, as well as their role in RNA condensate formation. The solubilities were also quantified after heat stress and recovery to investigate the condensate formation during heat stress response. Surprisingly. we found O-GlcNAc leads to dramatic solubility decrease of the modified proteins, and the degree of solubility drop is related to the protein localization and functions. Site-specific analysis found the adjacent residues and secondary structures of the glycosites are pivotal for the effect of O-GlcNAc for solubility change, and the number of acidic residues is related to the different effect of O-GlcNAc in heat stress and recovery. Additionally, it was found that O-GlcNAc promotes the dissociation of RNA condensates during heat stress, while it enhances the formation of RNA condensates in the recovery phase. The glycosites that facilitate the dissociation or the formation of the RNA condensates are distinct, and the physiological properties of their surroundings residues are diverse. This work advances our understanding of the role of O-GlcNAc in regulating biomolecular condensates and will be a useful resource for future research in biomolecular condensates.

2023-08-18 | MSV000092690 | MassIVE

Mediator promotes CENP-A incorporation at fission yeast centromeres [ChIP-seq]

2012-11-06 | GSE35524 | GEO

The Rpd3L HDAC complex is essential for the heat stress response in yeast

2010-04-23 | E-GEOD-17514 | biostudies-arrayexpress

CX-MS of TFIIH and Def1 complex

Project description:The DNA damage response is an essential process for the survival of living cells. In a subset of stress-responsive genes in humans,Elongin controls transcription in response to multiple stimuli, such as DNA damage, oxidative stress, and heat shock. Yeast Elongin (Ela1-Elc1), along with Def1, is known to facilitate ubiquitylation and degradation of RNA polymerase II (pol II) in response tomultiple stimuli, yet transcription activity has not been examined. We have found that Def1 copurifies from yeast whole-cell extract with TFIIH,the largest general transcription factor required for transcription initiation and nucleotide excision repair. The addition of recombinant Def1 and Ela1-Elc1 enhanced transcription initiation in an in vitro reconstituted system including pol II, the general transcription factors, and TFIIS. Def1 also enhanced transcription restart from TFIIS-induced cleavage in a pol II transcribing complex. In the Δdef1 strain, heat shock genes were misregulated, indicating that Def1 is required for induction of some stress-responsive genes in yeast. Taken together, our results extend the understanding of the molecular mechanism of transcription regulation on cellular stress and reveal functional similarities to the mammalian system.

2018-10-22 | PXD008223 | Pride

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